A lot of stereoscopic cameras use the .MPO format to store two JPEG images, including the Fuji W1, W3, and a few 3D camcorders that have a still mode. It can do two things for you: it can separate out the image files into a left and right pair, so you can process them or do whatever you want with them, or it can create an anaglyphic image (the ones you need coloured glasses to view). It is simple to use from the command line and takes wildcards, so you could process a whole batch of files with: mungempo *.MPO.
sbs_proc (Side by Side Processor) is a simple command-line application that processes side by side stereo images (such as those produced by some mobile phones) and converts them into monoscopic versions which can be visualised on non-stereo systems. It works on .jps files and produces .jpg outputs. It can produce anaglyph (red/blue glasses required) or right or left images.